1
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Stachura DL, Kalyvas JT, Abell AD. New Potent Sulfonamide-Based Inhibitors of S. aureus Biotin Protein Ligase. ACS Med Chem Lett 2024; 15:1467-1473. [PMID: 39291019 PMCID: PMC11403734 DOI: 10.1021/acsmedchemlett.4c00325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/29/2024] [Accepted: 08/29/2024] [Indexed: 09/19/2024] Open
Abstract
The key regulatory metabolic enzyme, biotin protein ligase (BPL), is an attractive target for the development of novel antibiotics against multi-drug-resistant bacteria, such as Staphylococcus aureus. Here we report the synthesis and assay of a new series of inhibitors (6-9) against S. aureus BPL (SaBPL), where a component sulfonamide linker was used to mimic the acyl-phosphate group of the natural intermediate biotinyl-5'-AMP (1). A pivotal correlation between the acidity of the central NH of the sulfonamide linker of 6-9 and in vitro inhibitory activity against SaBPL was observed. Specifically, sulfonylcarbamate 8, with its highly acidic sulfonyl central NH, as evaluated by 1H NMR spectroscopy, showed exceptional potency (K i = 10.3 ± 3.8 nM). Furthermore, three inhibitors demonstrated minimum inhibitory concentrations of 16-32 μg/mL against clinical methicillin-resistant S. aureus (MRSA) strains.
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Affiliation(s)
- Damian L Stachura
- Centre for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - John T Kalyvas
- Centre for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Andrew D Abell
- Centre for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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2
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Jeong KH, Son SB, Ko JH, Lee M, Lee JY. Structural insights into BirA from Haemophilus influenzae, a bifunctional protein as a biotin protein ligase and a transcriptional repressor. Biochem Biophys Res Commun 2024; 733:150601. [PMID: 39213703 DOI: 10.1016/j.bbrc.2024.150601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Biotin is an essential coenzyme involved in various metabolic processes across all known organisms, with biotinylation being crucial for the activity of carboxylases. BirA from Haemophilus influenzae is a bifunctional protein that acts as a biotin protein ligase and a transcriptional repressor. This study reveals the crystal structures of Hin BirA in both its apo- and holo-(biotinyl-5'-AMP bound) forms. As a class II BirA, it consists of three domains: N-terminal DNA binding domain, central catalytic domain, and C-terminal SH3-like domain. The structural analysis shows that the biotin-binding loop forms an ordered structure upon biotinyl-5'-AMP binding. This facilitates its interaction with the ligand and promotes protein dimerization. Comparative studies with other BirA homologs from different organisms indicate that the residues responsible for binding biotinyl-5'-AMP are highly conserved. This study also utilized AlphaFold2 to model the potential heterodimeric interaction between Hin BirA and biotin carboxyl carrier protein, thereby providing insights into the structural basis for biotinylation. These findings enhance our understanding of the structural and functional characteristics of Hin BirA, highlighting its potential as a target for novel antibiotics that disrupt the bacterial biotin synthesis pathways.
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Affiliation(s)
- Kang Hwa Jeong
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Su Bin Son
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Ji Hyuk Ko
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Minho Lee
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.
| | - Jae Young Lee
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.
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3
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Pathak T, Bose A. 1,5-disubstituted 1,2,3-triazolylated carbohydrates and nucleosides. Carbohydr Res 2024; 541:109126. [PMID: 38823061 DOI: 10.1016/j.carres.2024.109126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 06/03/2024]
Abstract
In general, 1,5-disubstituted 1,2,3-triazolyl moiety is much less common in the synthesis and applications in comparison to its regioisomeric counterpart. Moreover, the synthesis of 1,5-disubstituted 1,2,3-triazoles are not so straightforward as is the case for copper catalyzed strategy of 1,4-disubstituted 1,2,3-triazoles. The preparation of 1,5-triazolylated carbohydrates and nucleosides are even more complex because of the difficulties in accessing the appropriate starting materials as well as the compatibility of reaction conditions with the various protecting groups. 1,5-Disubstitution regioisomeric triazoles of carbohydrates and nucleosides were traditionally obtained as minor products through straightforward heating of the mixture of azides and terminal alkynes. However, the separation of isomers was tedious or in some cases futile. On the other hand, regioselective synthesis using ruthenium catalysis triggered serious concern of residual metal content in therapeutically important ingredients. Therefore, serious efforts are being made by several groups to develop non-toxic metal based or completely metal-free synthesis of 1,5-disubstituted 1,2,3-triazoles. This article strives to summarize the pre-Click era as well as the post-2001 reports on the synthesis and potential applications of 1,5-disubstituted 1,2,3-triazoles in biological systems.
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Affiliation(s)
- Tanmaya Pathak
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721 302, West Bengal, India.
| | - Amitabha Bose
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721 302, West Bengal, India
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4
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Yang P, Tian J, Zhang L, Zhang H, Yang G, Ren Y, Fang J, Gu Y, Jiang W. A toolbox for genetic manipulation in intestinal Clostridium symbiosum. Synth Syst Biotechnol 2024; 9:43-54. [PMID: 38234413 PMCID: PMC10793094 DOI: 10.1016/j.synbio.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/08/2023] [Accepted: 12/24/2023] [Indexed: 01/19/2024] Open
Abstract
Gut microbes are closely related with human health, but remain much to learn. Clostridium symbiosum is a conditionally pathogenic human gut bacterium and regarded as a potential biomarker for early diagnosis of intestinal tumors. However, the absence of an efficient toolbox that allows diverse genetic manipulations of this bacterium limits its in-depth studies. Here, we obtained the complete genome sequence of C. symbiosum ATCC 14940, a representative strain of C. symbiosum. On this basis, we further developed a series of genetic manipulation methods for this bacterium. Firstly, following the identification of a functional replicon pBP1 in C. symbiosum ATCC 14940, a highly efficient conjugative DNA transfer method was established, enabling the rapid introduction of exogenous plasmids into cells. Next, we constructed a dual-plasmid CRISPR/Cas12a system for genome editing in this bacterium, reaching over 60 % repression for most of the chosen genes as well as efficient deletion (>90 %) of three target genes. Finally, this toolbox was used for the identification of crucial functional genes, involving growth, synthesis of important metabolites, and virulence of C. symbiosum ATCC 14940. Our work has effectively established and optimized genome editing methods in intestinal C. symbiosum, thereby providing strong support for further basic and application research in this bacterium.
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Affiliation(s)
- Pengjie Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinzhong Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Xianghu Laboratory, Hangzhou, 311231, China
| | - Lu Zhang
- NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai, 200001, China
| | - Hui Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Gaohua Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Bruna Straket 16, Gothenburg, 41345, Sweden
| | - Yimeng Ren
- NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai, 200001, China
| | - Jingyuan Fang
- NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai, 200001, China
| | - Yang Gu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Weihong Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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5
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Farr DC, Haselhorst T, Tan L, Furness J, Strong E, Grice ID, West NP, Houston TA. Reassessing the putative molecular Target(s) of potent antitubercular 2-(Alkylsulfonyl)acetamides. Eur J Med Chem 2024; 264:115983. [PMID: 38048695 DOI: 10.1016/j.ejmech.2023.115983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/11/2023] [Accepted: 11/19/2023] [Indexed: 12/06/2023]
Abstract
Simple alkyl-sulfonylacetamides have potent antitubercular activity and significantly decrease mycolic acid levels in mycobacteria. Although these compounds were originally designed to inhibit the ketoacyl synthase domain of fatty acid synthase, structure-activity relationships and biochemical evidence do not fully support fatty acid synthase as the target. In 2004, an enzyme family involved in the activation and transfer of fatty acids as acyl-adenylates was identified in mycobacteria, separate from the universal acetyl-CoA carrier mechanism. These fatty acyl-AMP ligases (FAAL), encoded by the FadD family play important roles in the biosynthesis of mycolic acids along with fatty acid metabolism and are hypothesised here to be the molecular target of the sulfonylacetamides. Due to structural similarities with the ligase's natural substrate, it is believed these compounds are exerting action via competitive inhibition of these highly potent molecular targets. The primary aim of this investigation was to synthesize an extended library of sulfonylacetamide derivatives, building upon existing structural activity relations to validate the molecular mechanism with the aid of molecular modelling, while also attempting to explore novel structural isosteres for further drug design and development. Sulfonylacetamide derivatives were modified based on the putative molecular target resulting in derivatives with improved activities towards Mycobacteriumtuberculosis (H37Rv). The most active novel derivatives reported were 19, 22b, 22c and 46 displaying MIC90 levels of 1.4, 16.0, 13.0 and 5.9 μg/mL, respectively.
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Affiliation(s)
- Dylan C Farr
- Institute for Glycomics, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Juanelle Furness
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Emily Strong
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - I Darren Grice
- Institute for Glycomics, Griffith University, Gold Coast, QLD, 4222, Australia; School of Pharmacy and Medical Science, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Todd A Houston
- Institute for Glycomics, Griffith University, Gold Coast, QLD, 4222, Australia.
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6
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Ballari MS, O J Porta E, Zalazar EA, Etichetti CMB, Padrón JM, Girardini JE, Labadie GR. Lipophilic modification of salirasib modulates the antiproliferative and antimigratory activity. Bioorg Med Chem 2023; 92:117417. [PMID: 37531922 DOI: 10.1016/j.bmc.2023.117417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/11/2023] [Accepted: 07/16/2023] [Indexed: 08/04/2023]
Abstract
Salirasib, or farnesylthiosalicylic acid (FTS), is a salicylic acid derivative with demonstrated antineoplastic activity. While designed as a competitor of the substrate S-farnesyl cysteine on Ras, it is a potent competitive inhibitor of isoprenylcysteine carboxymethyl transferase. In this study, the antiproliferative activity on six different solid tumor cell lines was evaluated with a series of lipophilic thioether modified salirasib analogues, including those with or without a 1,2,3-triazole linker. A combination of bioassay, cheminformatics, docking, and in silico ADME-Tox was also performed. SAR analysis that analogues with three or more isoprene units or a long aliphatic chain exhibited the most potent activity. Furthermore, three compounds display superior antiproliferative activity than salirasib and similar potency compared to control anticancer drugs across all tested solid tumor cell lines. In addition, the behavior of the collection on migration and invasion, a key process in tumor metastasis, was also studied. Three analogues with specific antimigratory activity were identified with differential structural features being interesting starting points on the development of new antimetastatic agents. The antiproliferative and antimigratory effects observed suggest that modifying the thiol aliphatic/prenyl substituents can modulate the activity.
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Affiliation(s)
- María Sol Ballari
- Instituto de Química Rosario (IQUIR), Universidad Nacional de Rosario-CONICET, Suipacha 531 S2002LRK, Rosario, Argentina
| | - Exequiel O J Porta
- Instituto de Química Rosario (IQUIR), Universidad Nacional de Rosario-CONICET, Suipacha 531 S2002LRK, Rosario, Argentina
| | - Evelyn Arel Zalazar
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Suipacha 590 S2000LRJ, Rosario, Argentina
| | - Carla M Borini Etichetti
- Instituto de Fisiología Experimental de Rosario (IFISE-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531 2000 Rosario, Argentina
| | - José M Padrón
- BioLab, Instituto Universitario de Bio-Orgánica "Antonio González" (IUBO-AG), Universidad de La Laguna, Apartado 456 E-38071, La Laguna, Spain.
| | - Javier E Girardini
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Suipacha 590 S2000LRJ, Rosario, Argentina.
| | - Guillermo R Labadie
- Instituto de Química Rosario (IQUIR), Universidad Nacional de Rosario-CONICET, Suipacha 531 S2002LRK, Rosario, Argentina; Departamento de Química Orgánica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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7
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Mackie ERR, Barrow AS, Giel MC, Hulett MD, Gendall AR, Panjikar S, Soares da Costa TP. Repurposed inhibitor of bacterial dihydrodipicolinate reductase exhibits effective herbicidal activity. Commun Biol 2023; 6:550. [PMID: 37217566 DOI: 10.1038/s42003-023-04895-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
Herbicide resistance represents one of the biggest threats to our natural environment and agricultural sector. Thus, new herbicides are urgently needed to tackle the rise in herbicide-resistant weeds. Here, we employed a novel strategy to repurpose a 'failed' antibiotic into a new and target-specific herbicidal compound. Specifically, we identified an inhibitor of bacterial dihydrodipicolinate reductase (DHDPR), an enzyme involved in lysine biosynthesis in plants and bacteria, that exhibited no antibacterial activity but severely attenuated germination of the plant Arabidopsis thaliana. We confirmed that the inhibitor targets plant DHDPR orthologues in vitro, and exhibits no toxic effects against human cell lines. A series of analogues were then synthesised with improved efficacy in germination assays and against soil-grown A. thaliana. We also showed that our lead compound is the first lysine biosynthesis inhibitor with activity against both monocotyledonous and dicotyledonous weed species, by demonstrating its effectiveness at reducing the germination and growth of Lolium rigidum (rigid ryegrass) and Raphanus raphanistrum (wild radish). These results provide proof-of-concept that DHDPR inhibition may represent a much-needed new herbicide mode of action. Furthermore, this study exemplifies the untapped potential of repurposing 'failed' antibiotic scaffolds to fast-track the development of herbicide candidates targeting the respective plant enzymes.
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Affiliation(s)
- Emily R R Mackie
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Andrew S Barrow
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Marie-Claire Giel
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Mark D Hulett
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Anthony R Gendall
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC, 3168, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Tatiana P Soares da Costa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia.
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8
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Stachura D, Nguyen S, Polyak SW, Jovcevski B, Bruning JB, Abell AD. Structural Study of Potent Triazole-Based Inhibitors of Staphylococcus aureus Biotin Protein Ligase. ACS Med Chem Lett 2023; 14:285-290. [PMID: 36923924 PMCID: PMC10009792 DOI: 10.1021/acsmedchemlett.2c00505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/17/2023] [Indexed: 02/23/2023] Open
Abstract
The rise of multidrug-resistant bacteria, such as Staphylococcus aureus, has highlighted global urgency for new classes of antibiotics. Biotin protein ligase (BPL), a critical metabolic regulatory enzyme, is an important target that shows significant promise in this context. Here we report the in silico docking, synthesis, and biological assay of a new series of N1-diphenylmethyl-1,2,3-triazole-based S. aureus BPL (SaBPL) inhibitors (8-19) designed to probe the adenine binding site and define whole-cell activity for this important class of inhibitor. Triazoles 13 and 14 with N1-propylamine and -butanamide substituents, respectively, were particularly potent with K i values of 10 ± 2 and 30 ± 6 nM, respectively, against SaBPL. A strong correlation was apparent between the K i values for 8-19 and the in silico docking, with hydrogen bonding to amino acid residues S128 and N212 of SaBPL likely contributing to potent inhibition.
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Affiliation(s)
- Damian
L. Stachura
- Department
of Chemistry and Centre for Nanoscale BioPhotonics (CNBP) and
Institute of Photonics and Advanced Sensing (IPAS), School of Biological
Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Stephanie Nguyen
- Department
of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Steven W. Polyak
- UniSA
Clinical and Health Sciences, University
of South Australia, Adelaide, SA 5005, Australia
| | - Blagojce Jovcevski
- Department
of Chemistry and Centre for Nanoscale BioPhotonics (CNBP) and
Institute of Photonics and Advanced Sensing (IPAS), School of Biological
Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - John B. Bruning
- Department
of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Andrew D. Abell
- Department
of Chemistry and Centre for Nanoscale BioPhotonics (CNBP) and
Institute of Photonics and Advanced Sensing (IPAS), School of Biological
Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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9
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Samanta R, Sanghvi N, Beckett D, Matysiak S. Emergence of allostery through reorganization of protein residue network architecture. J Chem Phys 2023; 158:085104. [PMID: 36859102 PMCID: PMC9974213 DOI: 10.1063/5.0136010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Despite more than a century of study, consensus on the molecular basis of allostery remains elusive. A comparison of allosteric and non-allosteric members of a protein family can shed light on this important regulatory mechanism, and the bacterial biotin protein ligases, which catalyze post-translational biotin addition, provide an ideal system for such comparison. While the Class I bacterial ligases only function as enzymes, the bifunctional Class II ligases use the same structural architecture for an additional transcription repression function. This additional function depends on allosterically activated homodimerization followed by DNA binding. In this work, we used experimental, computational network, and bioinformatics analyses to uncover distinguishing features that enable allostery in the Class II biotin protein ligases. Experimental studies of the Class II Escherichia coli protein indicate that catalytic site residues are critical for both catalysis and allostery. However, allostery also depends on amino acids that are more broadly distributed throughout the protein structure. Energy-based community network analysis of representative Class I and Class II proteins reveals distinct residue community architectures, interactions among the communities, and responses of the network to allosteric effector binding. Bioinformatics mutual information analyses of multiple sequence alignments indicate distinct networks of coevolving residues in the two protein families. The results support the role of divergent local residue community network structures both inside and outside of the conserved enzyme active site combined with distinct inter-community interactions as keys to the emergence of allostery in the Class II biotin protein ligases.
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Affiliation(s)
- Riya Samanta
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - Neel Sanghvi
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - Dorothy Beckett
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
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10
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Synthesis, antimicrobial activity and molecular docking studies of spiroquinoline-indoline-dione and spiropyrazolo-indoline-dione derivatives. Sci Rep 2023; 13:1676. [PMID: 36717728 PMCID: PMC9885930 DOI: 10.1038/s41598-023-27777-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
Spiro[benzo[h]quinoline-7,3'-indoline]diones and spiro[indoline-3,4'-pyrazolo[3,4-b]quinoline]diones were efficiently synthesized via one-pot multi-component reactions under ultrasound-promoted conditions. Spiro[benzo[h]quinoline-7,3'-indoline]dione derivatives were successfully developed by the reaction of isatins, naphthalene-1-amine and 1,3-dicarbonyl compounds. The spiro[indoline-3,4'-pyrazolo[3,4-b]quinoline]dione derivatives were prepared by the reaction of isatins, 5-amino-1-methyl-3-pheylpyrazole, and 1,3-dicarbonyl compounds by using ( ±)-camphor-10-sulfonic acid as a catalyst in H2O/EtOH (3:1 v/v) solvent mixture. The antibacterial activity of the synthesized compounds was evaluated against, Enterococcus faecalis, Staphylococcus aureus and Candida albicans. Compounds 4b, 4h, and 6h showed the strongest antimicrobial activity toward both bacteria. The MIC values of these compounds ranged from 375-3000 µg/mL. The effect of these compounds (4b, 4h, 6h) as a function of applied dose and time was investigated by a kinetic study, and the interaction with these antimicrobial results was simulated by a molecular docking study. We also used the docking approach with Covid-19 since secondary bacterial infections. Docking showed that indoline-quinoline hybrid compounds 4b and 4h exerted the strongest docking binding value against the active sites of 6LU7. In addition, the synthesized compounds had a moderate to good free radical scavenging activity.
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11
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Synthesis of novel tetrazolic derivatives and evaluation of their antimicrobial activity. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.134913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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12
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Stachura DL, Nguyen S, Polyak SW, Jovcevski B, Bruning JB, Abell AD. A New 1,2,3-Triazole Scaffold with Improved Potency against Staphylococcus aureus Biotin Protein Ligase. ACS Infect Dis 2022; 8:2579-2585. [PMID: 36399035 DOI: 10.1021/acsinfecdis.2c00452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Staphylococcus aureus, a key ESKAPE bacteria, is responsible for most blood-based infections and, as a result, is a major economic healthcare burden requiring urgent attention. Here, we report in silico docking, synthesis, and assay of N1-diphenylmethyl triazole-based analogues (7-13) designed to interact with the entire binding site of S. aureus biotin protein ligase (SaBPL), an enzyme critical for the regulation of gluconeogenesis and fatty acid biosynthesis. The second aryl ring of these compounds enhances both SaBPL potency and whole cell activity against S. aureus relative to previously reported mono-benzyl triazoles. Analogues 12 and 13, with added substituents to better interact with the adenine binding site, are particularly potent, with Ki values of 6.01 ± 1.01 and 8.43 ± 0.73 nM, respectively. These analogues are the most active triazole-based inhibitors reported to date and, importantly, inhibit the growth of a clinical isolate strain of S. aureus ATCC 49775, with minimum inhibitory concentrations of 1 and 8 μg/mL, respectively.
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Affiliation(s)
- Damian L Stachura
- Department of Chemistry, School of Physical Sciences; Centre for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide5005, SA, Australia
| | - Stephanie Nguyen
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide5005, SA, Australia
| | - Steven W Polyak
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide5005, Australia
| | - Blagojce Jovcevski
- Department of Chemistry, School of Physical Sciences; Centre for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide5005, SA, Australia
| | - John B Bruning
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide5005, SA, Australia
| | - Andrew D Abell
- Department of Chemistry, School of Physical Sciences; Centre for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide5005, SA, Australia
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13
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Cherfi M, Harit T, Idrissi Yahyaoui M, Riahi A, Asehraou A, Malek F. Synthesis, antimicrobial activity and in-silico docking of two macrocycles based on pyrazole-tetrazole subunit. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Mather JC, Wyllie JA, Hamilton A, Soares da Costa TP, Barnard PJ. Antibacterial silver and gold complexes of imidazole and 1,2,4-triazole derived N-heterocyclic carbenes. Dalton Trans 2022; 51:12056-12070. [PMID: 35876319 DOI: 10.1039/d2dt01657e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of gold(I) (4a-4h, 5a-5b) and silver(I) (3a-3h) complexes of 1,2,4-triazolylidene and imidazolylidene based N-heterocyclic carbene ligands were prepared and the antibacterial activities of these complexes have been evaluated. The complexes were characterised using 1H-NMR, 13C-NMR, HRMS and in the cases of 3a, 3c, 4b and 5b by X-ray crystallography. The gold(I) complexes with phenyl substituents (4a-4d) were found to have potent antibacterial activity against Gram-positive bacteria, with the complexes of the 1,2,4-triazolylidene ligands being more active (4c, MIC = 4-8 μg mL-1 against Enterococcus faecium and 2 μg mL-1 against Staphylococcus aureus) than the analogous imidazolylidene complexes 4a and 4b (4a, MIC = 64 μg mL-1 against E. faecium and 2-4 μg mL-1 against S. aureus). Two of the silver(I) complexes have promising antibacterial activity against Acinetobacter baumannii (3f, MIC = 2-4 μg mL-1 and 3g, MIC = 2 μg mL-1). Silver(I) complex 3f and gold(I) complex 4c were tested against multi-drug resistant bacterial strains and high levels of antibacterial activity were observed. The potential for antibacterial resistance to develop against these metal containing complexes was investigated and significantly, no resistance was observed upon continuous treatment, whilst resistance was developed against the widely used broad-spectrum antibiotic ciprofloxacin in the same bacterial strains, under the conditions tested. The solution and gas phase stabilities of the complexes have been investigated using a combination of 1H-NMR, HRMS and detailed computational mechanistic studies were undertaken to gain insights into the possible decomposition reactions for silver complexes in aqueous solution.
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Affiliation(s)
- Joel C Mather
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia.
| | - Jessica A Wyllie
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia.
| | - Alex Hamilton
- Biomolecular Sciences Research Centre (BMRC) and Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia.
| | - Peter J Barnard
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia.
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15
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Naorem RS, Pangabam BD, Bora SS, Goswami G, Barooah M, Hazarika DJ, Fekete C. Identification of Putative Vaccine and Drug Targets against the Methicillin-Resistant Staphylococcus aureus by Reverse Vaccinology and Subtractive Genomics Approaches. Molecules 2022; 27:2083. [PMID: 35408485 PMCID: PMC9000511 DOI: 10.3390/molecules27072083] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 01/23/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an opportunistic pathogen and responsible for causing life-threatening infections. The emergence of hypervirulent and multidrug-resistant (MDR) S. aureus strains led to challenging issues in antibiotic therapy. Consequently, the morbidity and mortality rates caused by S. aureus infections have a substantial impact on health concerns. The current worldwide prevalence of MRSA infections highlights the need for long-lasting preventive measures and strategies. Unfortunately, effective measures are limited. In this study, we focus on the identification of vaccine candidates and drug target proteins against the 16 strains of MRSA using reverse vaccinology and subtractive genomics approaches. Using the reverse vaccinology approach, 4 putative antigenic proteins were identified; among these, PrsA and EssA proteins were found to be more promising vaccine candidates. We applied a molecular docking approach of selected 8 drug target proteins with the drug-like molecules, revealing that the ZINC4235426 as potential drug molecule with favorable interactions with the target active site residues of 5 drug target proteins viz., biotin protein ligase, HPr kinase/phosphorylase, thymidylate kinase, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase, and pantothenate synthetase. Thus, the identified proteins can be used for further rational drug or vaccine design to identify novel therapeutic agents for the treatment of multidrug-resistant staphylococcal infection.
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Affiliation(s)
- Romen Singh Naorem
- Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifusag utja. 6, 7624 Pecs, Hungary; (R.S.N.); (B.D.P.)
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India; (M.B.); (D.J.H.)
| | - Bandana Devi Pangabam
- Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifusag utja. 6, 7624 Pecs, Hungary; (R.S.N.); (B.D.P.)
| | - Sudipta Sankar Bora
- DBT—North East Centre for Agricultural Biotechnology (DBT-AAU Center), Assam Agricultural University, Jorhat 785013, India;
| | - Gunajit Goswami
- Multidisciplinary Research Unit, Jorhat Medical College and Hospital, Jorhat 785008, India;
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India; (M.B.); (D.J.H.)
- DBT—North East Centre for Agricultural Biotechnology (DBT-AAU Center), Assam Agricultural University, Jorhat 785013, India;
| | - Dibya Jyoti Hazarika
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India; (M.B.); (D.J.H.)
| | - Csaba Fekete
- Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifusag utja. 6, 7624 Pecs, Hungary; (R.S.N.); (B.D.P.)
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16
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Christoff RM, Soares da Costa TP, Bayat S, Holien JK, Perugini MA, Abbott BM. Synthesis and structure-activity relationship studies of 2,4-thiazolidinediones and analogous heterocycles as inhibitors of dihydrodipicolinate synthase. Bioorg Med Chem 2021; 52:116518. [PMID: 34826680 DOI: 10.1016/j.bmc.2021.116518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS), responsible for the first committed step of the diaminopimelate pathway for lysine biosynthesis, has become an attractive target for the development of new antibacterial and herbicidal agents. Herein, we report the discovery and exploration of the first inhibitors of E. coli DHDPS which have been identified from screening lead and are not based on substrates from the lysine biosynthesis pathway. Over 50 thiazolidinediones and related analogues have been prepared in order to thoroughly evaluate the structure-activity relationships against this enzyme of significant interest.
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Affiliation(s)
- Rebecca M Christoff
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Saadi Bayat
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Jessica K Holien
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3000, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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17
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Zhang C, Nie X, Zhang H, Wu Y, He H, Yang C, Jiang W, Gu Y. Functional dissection and modulation of the BirA protein for improved autotrophic growth of gas-fermenting Clostridium ljungdahlii. Microb Biotechnol 2021; 14:2072-2089. [PMID: 34291572 PMCID: PMC8449670 DOI: 10.1111/1751-7915.13884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/22/2021] [Indexed: 11/28/2022] Open
Abstract
Gas-fermenting Clostridium species can convert one-carbon gases (CO2 /CO) into a variety of chemicals and fuels, showing excellent application prospects in green biological manufacturing. The discovery of crucial genes and proteins with novel functions is important for understanding and further optimization of these autotrophic bacteria. Here, we report that the Clostridium ljungdahlii BirA protein (ClBirA) plays a pleiotropic regulator role, which, together with its biotin protein ligase (BPL) activity, enables an effective control of autotrophic growth of C. ljungdahlii. The structural modulation of ClBirA, combined with the in vivo and in vitro analyses, further reveals the action mechanism of ClBirA's dual roles as well as their interaction in C. ljungdahlii. Importantly, an atypical, flexible architecture of the binding site was found to be employed by ClBirA in the regulation of a lot of essential pathway genes, thereby expanding BirA's target genes to a broader range in clostridia. Based on these findings, molecular modification of ClBirA was performed, and an improved cellular performance of C. ljungdahlii was achieved in gas fermentation. This work reveals a previously unknown potent role of BirA in gas-fermenting clostridia, providing new perspective for understanding and engineering these autotrophic bacteria.
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Affiliation(s)
- Can Zhang
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoqun Nie
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Huan Zhang
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- University of Chinese Academy of SciencesBeijingChina
| | - Yuwei Wu
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- University of Chinese Academy of SciencesBeijingChina
| | - Huiqi He
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Chen Yang
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Weihong Jiang
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Yang Gu
- Key Laboratory of Synthetic BiologyThe State Key Laboratory of Plant Carbon‐Nitrogen AssimilationCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
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18
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Soares da Costa TP, Hall CJ, Panjikar S, Wyllie JA, Christoff RM, Bayat S, Hulett MD, Abbott BM, Gendall AR, Perugini MA. Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants. eLife 2021; 10:69444. [PMID: 34313586 PMCID: PMC8341977 DOI: 10.7554/elife.69444] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/27/2021] [Indexed: 11/29/2022] Open
Abstract
Weeds are becoming increasingly resistant to our current herbicides, posing a significant threat to agricultural production. Therefore, new herbicides with novel modes of action are urgently needed. In this study, we exploited a novel herbicide target, dihydrodipicolinate synthase (DHDPS), which catalyses the first and rate-limiting step in lysine biosynthesis. The first class of plant DHDPS inhibitors with micromolar potency against Arabidopsis thaliana DHDPS was identified using a high-throughput chemical screen. We determined that this class of inhibitors binds to a novel and unexplored pocket within DHDPS, which is highly conserved across plant species. The inhibitors also attenuated the germination and growth of A. thaliana seedlings and confirmed their pre-emergence herbicidal activity in soil-grown plants. These results provide proof-of-concept that lysine biosynthesis represents a promising target for the development of herbicides with a novel mode of action to tackle the global rise of herbicide-resistant weeds.
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Affiliation(s)
- Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Cody J Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Jessica A Wyllie
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Rebecca M Christoff
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Saadi Bayat
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Mark D Hulett
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Anthony R Gendall
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, Australia.,Australian Research Council Research Hub for Medicinal Agriculture, Bundoora, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
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19
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Martín-Serrano Á, Gonzalez-Morena JM, Barbero N, Ariza A, Sánchez Gómez FJ, Pérez-Inestrosa E, Pérez-Sala D, Torres MJ, Montañez MI. Biotin-Labelled Clavulanic Acid to Identify Proteins Target for Haptenation in Serum: Implications in Allergy Studies. Front Pharmacol 2021; 11:594755. [PMID: 33442385 PMCID: PMC7797785 DOI: 10.3389/fphar.2020.594755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/06/2020] [Indexed: 12/19/2022] Open
Abstract
Clavulanic acid (CLV) and amoxicillin, frequently administered in combination, can be independently involved in allergic reactions. Protein haptenation with β-lactams is considered necessary to activate the immune system. The aim of this study was to assess the suitability of biotinylated analogues of CLV as probes to study protein haptenation by this β-lactam. Two synthetic approaches afforded the labeling of CLV through esterification of its carboxylic group with a biotin moiety, via either direct binding (CLV-B) or tetraethylenglycol linker (CLV-TEG-B). The second analogue offered advantages as solubility in aqueous solution and potential lower steric hindrance for both intended interactions, with the protein and with avidin. NMR reactivity studies showed that both CLV and CLV-TEG-B reacts through β-lactam ring opening by aliphatic amino nitrogen, however with different stability of resulting conjugates. Unlike CLV conjugates, that promoted the decomposition of clavulanate fragment, the conjugates obtained with the CLV-TEG-B remained linked, as a whole structure including biotin, to nucleophile and showed a better stability. This was a desired key feature to allow CLV-TEG-B conjugated protein detection at great sensitivity. We have used biotin detection and mass spectrometry (MS) to detect the haptenation of human serum albumin (HSA) and human serum proteins. MS of conjugates showed that HSA could be modified by CLV-TEG-B. Remarkably, HSA preincubation with CLV excess only reduced moderately the incorporation of CLV-TEG-B, which could be attributed to different protein interferences. The CLV-TEG-B fragment with opened β-lactam was detected bound to the 404-430HSA peptide of the treated protein. Incubation of human serum with CLV-TEG-B resulted in the haptenation of several proteins that were identified by 2D-electrophoresis and peptide mass fingerprinting as HSA, haptoglobin, and heavy and light chains of immunoglobulins. Taken together, our results show that tagged-CLV keeps some of the CLV features. Moreover, although we observe a different behavior in the conjugate stability and in the site of protein modification, the similar reactivity indicates that it could constitute a valuable tool to identify protein targets for haptenation by CLV with high sensitivity to get insights into the activation of the immune system by CLV and mechanisms involved in β-lactams allergy.
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Affiliation(s)
- Ángela Martín-Serrano
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain.,Centro Andaluz de Nanomedicina y Biotecnología-BIONAND, Málaga, Spain
| | - Juan M Gonzalez-Morena
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Nekane Barbero
- Centro Andaluz de Nanomedicina y Biotecnología-BIONAND, Málaga, Spain.,Department Química Orgánica, Universidad de Málaga-IBIMA, Málaga, Spain
| | - Adriana Ariza
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain
| | - Francisco J Sánchez Gómez
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Ezequiel Pérez-Inestrosa
- Centro Andaluz de Nanomedicina y Biotecnología-BIONAND, Málaga, Spain.,Department Química Orgánica, Universidad de Málaga-IBIMA, Málaga, Spain
| | - Dolores Pérez-Sala
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Maria J Torres
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain.,Centro Andaluz de Nanomedicina y Biotecnología-BIONAND, Málaga, Spain.,Allergy Unit, Hospital Regional Universitario de Málaga, Málaga, Spain.,Department of Medicina, Universidad de Málaga, Málaga, Spain
| | - María I Montañez
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain.,Centro Andaluz de Nanomedicina y Biotecnología-BIONAND, Málaga, Spain
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20
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Sternicki LM, Nguyen S, Pacholarz KJ, Barran P, Pendini NR, Booker GW, Huet Y, Baltz R, Wegener KL, Pukala TL, Polyak SW. Biochemical characterisation of class III biotin protein ligases from Botrytis cinerea and Zymoseptoria tritici. Arch Biochem Biophys 2020; 691:108509. [PMID: 32717225 DOI: 10.1016/j.abb.2020.108509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
Biotin protein ligase (BPL) is an essential enzyme in all kingdoms of life, making it a potential target for novel anti-infective agents. Whilst bacteria and archaea have simple BPL structures (class I and II), the homologues from certain eukaryotes such as mammals, insects and yeast (class III) have evolved a more complex structure with a large extension on the N-terminus of the protein in addition to the conserved catalytic domain. The absence of atomic resolution structures of any class III BPL hinders structural and functional analysis of these enzymes. Here, two new class III BPLs from agriculturally important moulds Botrytis cinerea and Zymoseptoria tritici were characterised alongside the homologue from the prototypical yeast Saccharomyces cerevisiae. Circular dichroism and ion mobility-mass spectrometry analysis revealed conservation of the overall tertiary and secondary structures of all three BPLs, corresponding with the high sequence similarity. Subtle structural differences were implied by the different thermal stabilities of the enzymes and their varied Michaelis constants for their interactions with ligands biotin, MgATP, and biotin-accepting substrates from different species. The three BPLs displayed different preferences for fungal versus bacterial protein substrates, providing further evidence that class III BPLs have a 'substrate validation' activity for selecting only appropriate proteins for biotinylation. Selective, potent inhibition of these three BPLs was demonstrated despite sequence and structural homology. This highlights the potential for targeting BPL for novel, selective antifungal therapies against B. cinerea, Z. tritici and other fungal species.
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Affiliation(s)
- Louise M Sternicki
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Stephanie Nguyen
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia
| | - Kamila J Pacholarz
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicole R Pendini
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Grant W Booker
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Yoann Huet
- Bayer SAS CropScience, La Dargoire Research Centre, Lyon, 69263 Cedex 09, France
| | - Rachel Baltz
- Bayer SAS CropScience, La Dargoire Research Centre, Lyon, 69263 Cedex 09, France
| | - Kate L Wegener
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia
| | - Tara L Pukala
- School of Physical Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Steven W Polyak
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia.
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21
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Bockman MR, Mishra N, Aldrich CC. The Biotin Biosynthetic Pathway in Mycobacterium tuberculosis is a Validated Target for the Development of Antibacterial Agents. Curr Med Chem 2020; 27:4194-4232. [PMID: 30663561 DOI: 10.2174/0929867326666190119161551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 01/12/2019] [Indexed: 12/11/2022]
Abstract
Mycobacterium tuberculosis, responsible for Tuberculosis (TB), remains the leading cause of mortality among infectious diseases worldwide from a single infectious agent, with an estimated 1.7 million deaths in 2016. Biotin is an essential cofactor in M. tuberculosis that is required for lipid biosynthesis and gluconeogenesis. M. tuberculosis relies on de novo biotin biosynthesis to obtain this vital cofactor since it cannot scavenge sufficient biotin from a mammalian host. The biotin biosynthetic pathway in M. tuberculosis has been well studied and rigorously genetically validated providing a solid foundation for medicinal chemistry efforts. This review examines the mechanism and structure of the enzymes involved in biotin biosynthesis and ligation, summarizes the reported genetic validation studies of the pathway, and then analyzes the most promising inhibitors and natural products obtained from structure-based drug design and phenotypic screening.
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Affiliation(s)
- Matthew R Bockman
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Neeraj Mishra
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
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22
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Hayes AJ, Satiaputra J, Sternicki LM, Paparella AS, Feng Z, Lee KJ, Blanco-Rodriguez B, Tieu W, Eijkelkamp BA, Shearwin KE, Pukala TL, Abell AD, Booker GW, Polyak SW. Advanced Resistance Studies Identify Two Discrete Mechanisms in Staphylococcus aureus to Overcome Antibacterial Compounds that Target Biotin Protein Ligase. Antibiotics (Basel) 2020; 9:antibiotics9040165. [PMID: 32268615 PMCID: PMC7235819 DOI: 10.3390/antibiotics9040165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 11/16/2022] Open
Abstract
Biotin protein ligase (BPL) inhibitors are a novel class of antibacterial that target clinically important methicillin-resistant Staphylococcus aureus (S. aureus). In S. aureus, BPL is a bifunctional protein responsible for enzymatic biotinylation of two biotin-dependent enzymes, as well as serving as a transcriptional repressor that controls biotin synthesis and import. In this report, we investigate the mechanisms of action and resistance for a potent anti-BPL, an antibacterial compound, biotinyl-acylsulfamide adenosine (BASA). We show that BASA acts by both inhibiting the enzymatic activity of BPL in vitro, as well as functioning as a transcription co-repressor. A low spontaneous resistance rate was measured for the compound (<10−9) and whole-genome sequencing of strains evolved during serial passaging in the presence of BASA identified two discrete resistance mechanisms. In the first, deletion of the biotin-dependent enzyme pyruvate carboxylase is proposed to prioritize the utilization of bioavailable biotin for the essential enzyme acetyl-CoA carboxylase. In the second, a D200E missense mutation in BPL reduced DNA binding in vitro and transcriptional repression in vivo. We propose that this second resistance mechanism promotes bioavailability of biotin by derepressing its synthesis and import, such that free biotin may outcompete the inhibitor for binding BPL. This study provides new insights into the molecular mechanisms governing antibacterial activity and resistance of BPL inhibitors in S. aureus.
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Affiliation(s)
- Andrew J. Hayes
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Jiulia Satiaputra
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Louise M. Sternicki
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Ashleigh S. Paparella
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Zikai Feng
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Kwang J. Lee
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - Beatriz Blanco-Rodriguez
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - William Tieu
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - Bart A. Eijkelkamp
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Keith E. Shearwin
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Tara L. Pukala
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
| | - Andrew D. Abell
- School of Physical Sciences, University of Adelaide, South Australia 5005, Australia; (K.J.L.); (B.B.-R.); (W.T.); (T.L.P.); (A.D.A.)
- Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, SA 5005, Australia
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Grant W. Booker
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
| | - Steven W. Polyak
- School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; (A.J.H.); (J.S.); (L.M.S.); (A.S.P.); (Z.F.); (B.A.E.); (K.E.S.); (G.W.B.)
- Correspondence: ; Tel.: +61883021603
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23
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Li Z, Mackie ERR, Ramkissoon P, Mather JC, Wiratpruk N, Soares da Costa TP, Barnard PJ. Synthesis, conformational analysis and antibacterial activity of Au(i)–Ag(i) and Au(i)–Hg(ii) heterobimetallic N-heterocyclic carbene complexes. Dalton Trans 2020; 49:12820-12834. [DOI: 10.1039/d0dt02225j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A family heterobimetallic Au(i)–Ag(i) and Au(i)–Hg(ii) complexes of bis-N-heterocyclic carbene ligands been prepared and their antibacterial properties evaluated.
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Affiliation(s)
- Zili Li
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Australia
| | - Emily R. R. Mackie
- Department of Biochemistry and Genetics
- La Trobe Institute for Molecular Science
- La Trobe University
- Australia
| | - Pria Ramkissoon
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Australia
| | - Joel C. Mather
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Australia
| | - Nuchareenat Wiratpruk
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Australia
| | - Tatiana P. Soares da Costa
- Department of Biochemistry and Genetics
- La Trobe Institute for Molecular Science
- La Trobe University
- Australia
| | - Peter J. Barnard
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Australia
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24
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Lee KJ, Tieu W, Blanco-Rodriguez B, Paparella AS, Yu J, Hayes A, Feng J, Marshall AC, Noll B, Milne R, Cini D, Wilce MCJ, Booker GW, Bruning JB, Polyak SW, Abell AD. Sulfonamide-Based Inhibitors of Biotin Protein Ligase as New Antibiotic Leads. ACS Chem Biol 2019; 14:1990-1997. [PMID: 31407891 DOI: 10.1021/acschembio.9b00463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we report the design, synthesis, and evaluation of a series of inhibitors of Staphylococcus aureus BPL (SaBPL), where the central acyl phosphate of the natural intermediate biotinyl-5'-AMP (1) is replaced by a sulfonamide isostere. Acylsulfamide (6) and amino sulfonylurea (7) showed potent in vitro inhibitory activity (Ki = 0.007 ± 0.003 and 0.065 ± 0.03 μM, respectively) and antibacterial activity against S. aureus ATCC49775 with minimum inhibitory concentrations of 0.25 and 4 μg/mL, respectively. Additionally, the bimolecular interactions between the BPL and inhibitors 6 and 7 were defined by X-ray crystallography and molecular dynamics simulations. The high acidity of the sulfonamide linkers of 6 and 7 likely contributes to the enhanced in vitro inhibitory activities by promoting interaction with SaBPL Lys187. Analogues with alkylsulfamide (8), β-ketosulfonamide (9), and β-hydroxysulfonamide (10) isosteres were devoid of significant activity. Binding free energy estimation using computational methods suggests deprotonated 6 and 7 to be the best binders, which is consistent with enzyme assay results. Compound 6 was unstable in whole blood, leading to poor pharmacokinetics. Importantly, 7 has a vastly improved pharmacokinetic profile compared to that of 6 presumably due to the enhanced metabolic stability of the sulfonamide linker moiety.
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Affiliation(s)
- Kwang Jun Lee
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | - William Tieu
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Beatriz Blanco-Rodriguez
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ashleigh S. Paparella
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jingxian Yu
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew Hayes
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jiage Feng
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew C. Marshall
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Benjamin Noll
- School of Pharmacy & Medical Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Robert Milne
- School of Pharmacy & Medical Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Danielle Cini
- Department of Biochemistry, School of Biomedical Science, Monash University, Clayton, Victoria 3800, Australia
| | - Matthew C. J. Wilce
- Department of Biochemistry, School of Biomedical Science, Monash University, Clayton, Victoria 3800, Australia
| | - Grant W. Booker
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John B. Bruning
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Steven W. Polyak
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D. Abell
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
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25
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Evans CE, Si Y, Matarlo JS, Yin Y, French JB, Tonge PJ, Tan DS. Structure-Based Design, Synthesis, and Biological Evaluation of Non-Acyl Sulfamate Inhibitors of the Adenylate-Forming Enzyme MenE. Biochemistry 2019; 58:1918-1930. [PMID: 30912442 PMCID: PMC6653581 DOI: 10.1021/acs.biochem.9b00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
N-Acyl sulfamoyladenosines (acyl-AMS) have been used
extensively to inhibit adenylate-forming enzymes that are involved in a wide
range of biological processes. These acyl-AMS inhibitors are nonhydrolyzable
mimics of the cognate acyl adenylate intermediates that are bound tightly by
adenylate-forming enzymes. However, the anionic acyl sulfamate moiety presents a
pharmacological liability that may be detrimental to cell permeability and
pharmacokinetic profiles. We have previously developed the acyl sulfamate
OSB-AMS (1) as a potent inhibitor of the adenylate-forming enzyme
MenE, an o-succinylbenzoate-CoA (OSB-CoA) synthetase that is
required for bacterial menaquinone biosynthesis. Herein, we report the use of
computational docking to develop novel, non-acyl sulfamate inhibitors of MenE. A
m-phenyl ether-linked analogue (5) was found
to be the most potent inhibitor (IC50 = 8 μM;
Kd = 244 nM), and its X-ray co-crystal structure
was determined to characterize its binding mode in comparison to the
computational prediction. This work provides a framework for the development of
potent non-acyl sulfamate inhibitors of other adenylate-forming enzymes in the
future.
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26
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Satiaputra J, Sternicki LM, Hayes AJ, Pukala TL, Booker GW, Shearwin KE, Polyak SW. Native mass spectrometry identifies an alternative DNA-binding pathway for BirA from Staphylococcus aureus. Sci Rep 2019; 9:2767. [PMID: 30808984 PMCID: PMC6391492 DOI: 10.1038/s41598-019-39398-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/15/2019] [Indexed: 11/09/2022] Open
Abstract
An adequate supply of biotin is vital for the survival and pathogenesis of Staphylococcus aureus. The key protein responsible for maintaining biotin homeostasis in bacteria is the biotin retention protein A (BirA, also known as biotin protein ligase). BirA is a bi-functional protein that serves both as a ligase to catalyse the biotinylation of important metabolic enzymes, as well as a transcriptional repressor that regulates biotin biosynthesis, biotin transport and fatty acid elongation. The mechanism of BirA regulated transcription has been extensively characterized in Escherichia coli, but less so in other bacteria. Biotin-induced homodimerization of E. coli BirA (EcBirA) is a necessary prerequisite for stable DNA binding and transcriptional repression. Here, we employ a combination of native mass spectrometry, in vivo gene expression assays, site-directed mutagenesis and electrophoretic mobility shift assays to elucidate the DNA binding pathway for S. aureus BirA (SaBirA). We identify a mechanism that differs from that of EcBirA, wherein SaBirA is competent to bind DNA as a monomer both in the presence and absence of biotin and/or MgATP, allowing homodimerization on the DNA. Bioinformatic analysis demonstrated the SaBirA sequence used here is highly conserved amongst other S. aureus strains, implying this DNA-binding mechanism is widely employed.
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Affiliation(s)
- Jiulia Satiaputra
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Harry Perkins Institute of Medical Research, Shenton Park, Western Australia, 6008, Australia
| | - Louise M Sternicki
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Andrew J Hayes
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Faculty of Health and Medical Sciences, Adelaide, South Australia, 5005, Australia
| | - Tara L Pukala
- School of Physical Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Grant W Booker
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Keith E Shearwin
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Steven W Polyak
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia.
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, 5001, Australia.
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27
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Paparella AS, Feng J, Blanco-Rodriguez B, Feng Z, Phetsang W, Blaskovich MA, Cooper MA, Booker GW, Polyak SW, Abell AD. A template guided approach to generating cell permeable inhibitors of Staphylococcus aureus biotin protein ligase. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.10.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Paparella AS, Lee KJ, Hayes AJ, Feng J, Feng Z, Cini D, Deshmukh S, Booker GW, Wilce MCJ, Polyak SW, Abell AD. Halogenation of Biotin Protein Ligase Inhibitors Improves Whole Cell Activity against Staphylococcus aureus. ACS Infect Dis 2018; 4:175-184. [PMID: 29131575 DOI: 10.1021/acsinfecdis.7b00134] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report the synthesis and evaluation of 5-halogenated-1,2,3-triazoles as inhibitors of biotin protein ligase from Staphylococcus aureus. The halogenated compounds exhibit significantly improved antibacterial activity over their nonhalogenated counterparts. Importantly, the 5-fluoro-1,2,3-triazole compound 4c displays antibacterial activity against S. aureus ATCC49775 with a minimum inhibitory concentration (MIC) of 8 μg/mL.
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Affiliation(s)
- Ashleigh S. Paparella
- Department of Molecular
and Cellular Biology, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Kwang Jun Lee
- Department of Chemistry, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Andrew J. Hayes
- Department of Molecular
and Cellular Biology, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Jiage Feng
- Department of Chemistry, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
- Centre
for Nanoscale BioPhotonics (CNBP), University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Zikai Feng
- Department of Molecular
and Cellular Biology, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Danielle Cini
- School of Biomedical Science, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Sonali Deshmukh
- Department of Molecular
and Cellular Biology, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Grant W. Booker
- Department of Molecular
and Cellular Biology, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Matthew C. J. Wilce
- School of Biomedical Science, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Steven W. Polyak
- Department of Molecular
and Cellular Biology, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
| | - Andrew D. Abell
- Department of Chemistry, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
- Centre
for Nanoscale BioPhotonics (CNBP), University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia
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29
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A green fluorescent protein-based assay for high-throughput ligand-binding studies of a mycobacterial biotin protein ligase. Microbiol Res 2017; 205:35-39. [PMID: 28942842 DOI: 10.1016/j.micres.2017.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 01/06/2023]
Abstract
Biotin protein ligase (BirA) has been identified as an emerging drug target in Mycobacterium tuberculosis due to its essential metabolic role. Indeed, it is the only enzyme capable of covalently attaching biotin onto the biotin carboxyl carrier protein subunit of the acetyl-CoA carboxylase. Despite recent interest in this protein, there is still a gap in cost-effective high-throughput screening assays for rapid identification of mycobacterial BirA-targeting inhibitors. We present for the first time the cloning, expression, purification of mycobacterial GFP-tagged BirA and its application for the development of a high-throughput assay building on the principle of differential scanning fluorimetry of GFP-tagged proteins. The data obtained in this study reveal how biotin and ATP significantly increase the thermal stability (ΔTm=+16.5°C) of M. tuberculosis BirA and lead to formation of a high affinity holoenzyme complex (Kobs=7.7nM). The new findings and mycobacterial BirA high-throughput assay presented in this work could provide an efficient platform for future anti-tubercular drug discovery campaigns.
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30
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Soares da Costa TP, Patel M, Desbois S, Gupta R, Faou P, Perugini MA. Identification of a dimeric KDG aldolase from
Agrobacterium tumefaciens. Proteins 2017; 85:2058-2065. [DOI: 10.1002/prot.25359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Tatiana P. Soares da Costa
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe UniversityMelbourne Victoria Australia
| | - Madhvi Patel
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe UniversityMelbourne Victoria Australia
| | - Sebastien Desbois
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe UniversityMelbourne Victoria Australia
| | - Ruchi Gupta
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe UniversityMelbourne Victoria Australia
| | - Pierre Faou
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe UniversityMelbourne Victoria Australia
| | - Matthew A. Perugini
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe UniversityMelbourne Victoria Australia
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31
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Bonandi E, Christodoulou MS, Fumagalli G, Perdicchia D, Rastelli G, Passarella D. The 1,2,3-triazole ring as a bioisostere in medicinal chemistry. Drug Discov Today 2017; 22:1572-1581. [PMID: 28676407 DOI: 10.1016/j.drudis.2017.05.014] [Citation(s) in RCA: 410] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/16/2017] [Accepted: 05/25/2017] [Indexed: 10/25/2022]
Abstract
1,2,3-Triazole is a well-known scaffold that has a widespread occurrence in different compounds characterized by several bioactivities, such as antimicrobial, antiviral, and antitumor effects. Moreover, the structural features of 1,2,3-triazole enable it to mimic different functional groups, justifying its wide use as a bioisostere for the synthesis of new active molecules. Here, we provide an overview of the 1,2,3-triazole ring as a bioisostere for the design of drug analogs, highlighting relevant recent examples.
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Affiliation(s)
- Elisa Bonandi
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Michael S Christodoulou
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy; Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Gaia Fumagalli
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Dario Perdicchia
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Giulio Rastelli
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Daniele Passarella
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy.
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32
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Mechanisms Governing Precise Protein Biotinylation. Trends Biochem Sci 2017; 42:383-394. [DOI: 10.1016/j.tibs.2017.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/25/2017] [Accepted: 02/03/2017] [Indexed: 12/26/2022]
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33
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Bond TEH, Sorenson AE, Schaeffer PM. Functional characterisation of Burkholderia pseudomallei biotin protein ligase: A toolkit for anti-melioidosis drug development. Microbiol Res 2017; 199:40-48. [PMID: 28454708 DOI: 10.1016/j.micres.2017.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/06/2017] [Accepted: 03/15/2017] [Indexed: 01/17/2023]
Abstract
Burkholderia pseudomallei (Bp) is the causative agent of melioidosis. The bacterium is responsible for 20% of community-acquired sepsis cases and 40% of sepsis-related mortalities in northeast Thailand, and is intrinsically resistant to aminoglycosides, macrolides, rifamycins, cephalosporins, and nonureidopenicillins. There is no vaccine and its diagnosis is problematic. Biotin protein ligase (BirA) which is essential for fatty acid synthesis has been proposed as a drug target in bacteria. Very few bacterial BirA have been characterized, and a better understanding of these enzymes is necessary to further assess their value as drug targets. BirA within the Burkholderia genus have not yet been investigated. We present for the first time the cloning, expression, purification and functional characterisation of the putative Bp BirA and orthologous B. thailandensis (Bt) biotin carboxyl carrier protein (BCCP) substrate. A GFP-tagged Bp BirA was produced and applied for the development of a high-throughput (HT) assay based on our differential scanning fluorimetry of GFP-tagged proteins (DSF-GTP) principle as well as an electrophoretic mobility shift assay. Our biochemical data in combination with the new HT DSF-GTP and biotinylation activity assay could facilitate future drug screening efforts against this drug-resistant organism.
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Affiliation(s)
- Thomas E H Bond
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia
| | - Alanna E Sorenson
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia
| | - Patrick M Schaeffer
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia.
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34
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Feng J, Paparella AS, Tieu W, Heim D, Clark S, Hayes A, Booker GW, Polyak SW, Abell AD. New Series of BPL Inhibitors To Probe the Ribose-Binding Pocket of Staphylococcus aureus Biotin Protein Ligase. ACS Med Chem Lett 2016; 7:1068-1072. [PMID: 27994739 DOI: 10.1021/acsmedchemlett.6b00248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/10/2016] [Indexed: 01/11/2023] Open
Abstract
Replacing the labile adenosinyl-substituted phosphoanhydride of biotinyl-5'-AMP with a N1-benzyl substituted 1,2,3-triazole gave a new truncated series of inhibitors of Staphylococcus aureus biotin protein ligase (SaBPL). The benzyl group presents to the ribose-binding pocket of SaBPL based on in silico docking. Halogenated benzyl derivatives (12t, 12u, 12w, and 12x) proved to be the most potent inhibitors of SaBPL. These derivatives inhibited the growth of S. aureus ATCC49775 and displayed low cytotoxicity against HepG2 cells.
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Affiliation(s)
- Jiage Feng
- Department of Chemistry, §Department of Molecular and Cellular Biology, and ‡Centre for Nanoscale
BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - William Tieu
- Department of Chemistry, §Department of Molecular and Cellular Biology, and ‡Centre for Nanoscale
BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Sarah Clark
- Department of Chemistry, §Department of Molecular and Cellular Biology, and ‡Centre for Nanoscale
BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | | | | | - Andrew D. Abell
- Department of Chemistry, §Department of Molecular and Cellular Biology, and ‡Centre for Nanoscale
BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
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35
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Henke SK, Cronan JE. The Staphylococcus aureus group II biotin protein ligase BirA is an effective regulator of biotin operon transcription and requires the DNA binding domain for full enzymatic activity. Mol Microbiol 2016; 102:417-429. [PMID: 27445042 PMCID: PMC5116234 DOI: 10.1111/mmi.13470] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2016] [Indexed: 11/30/2022]
Abstract
Group II biotin protein ligases (BPLs) are characterized by the presence of an N-terminal DNA binding domain that functions in transcriptional regulation of the genes of biotin biosynthesis and transport. The Staphylococcus aureus Group II BPL which is called BirA has been reported to bind an imperfect inverted repeat located upstream of the biotin synthesis operon. DNA binding by other Group II BPLs requires dimerization of the protein which is triggered by synthesis of biotinoyl-AMP (biotinoyl-adenylate), the intermediate in the ligation of biotin to its cognate target proteins. However, the S. aureus BirA was reported to dimerize and bind DNA in the absence of biotin or biotinoyl-AMP (Soares da Costa et al. (2014) Mol Microbiol 91: 110-120). These in vitro results argued that the protein would be unable to respond to the levels of biotin or acceptor proteins and thus would lack the regulatory properties of the other characterized BirA proteins. We tested the regulatory function of the protein using an in vivo model system and examined its DNA binding properties in vitro using electrophoretic mobility shift and fluorescence anisotropy analyses. We report that the S. aureus BirA is an effective regulator of biotin operon transcription and that the prior data can be attributed to artifacts of mobility shift analyses. We also report that deletion of the DNA binding domain of the S. aureus BirA results in loss of virtually all of its ligation activity.
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Affiliation(s)
- Sarah K Henke
- Departments of Microbiology, University of Illinois, Urbana, Illinois, 61801, USA
| | - John E Cronan
- Departments of Microbiology, University of Illinois, Urbana, Illinois, 61801, USA.
- Biochemistry, University of Illinois, Urbana, Illinois, 61801, USA.
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Antitubercular activity of 1,2,3-triazolyl fatty acid derivatives. Eur J Med Chem 2016; 125:842-852. [PMID: 27750201 DOI: 10.1016/j.ejmech.2016.09.086] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/24/2016] [Accepted: 09/26/2016] [Indexed: 12/27/2022]
Abstract
A collection of 1,2,3-triazoles unsaturated fatty acid mimics were efficiently synthesized by click chemistry. The 1,4-disubstituted analogs prepared covered different alkyl chain lengths and triazole positions. The compounds were subsequently tested against Mycobacterium tuberculosis, being most of them active with some of the analogs displaying activity at micromolar concentration. The most potent member of the series has the triazole moiety on the C-2 position with a carbon chain of eight or ten carbon atoms. The 1,5-isomers of the most active analog were significantly less active than the original isomer. The activity of the selected hit was assayed on several clinical MTB multi-drug resistant strains providing the same MIC.
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37
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Biotin Protein Ligase Is a Target for New Antibacterials. Antibiotics (Basel) 2016; 5:antibiotics5030026. [PMID: 27463729 PMCID: PMC5039522 DOI: 10.3390/antibiotics5030026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/02/2022] Open
Abstract
There is a desperate need for novel antibiotic classes to combat the rise of drug resistant pathogenic bacteria, such as Staphylococcus aureus. Inhibitors of the essential metabolic enzyme biotin protein ligase (BPL) represent a promising drug target for new antibacterials. Structural and biochemical studies on the BPL from S. aureus have paved the way for the design and development of new antibacterial chemotherapeutics. BPL employs an ordered ligand binding mechanism for the synthesis of the reaction intermediate biotinyl-5′-AMP from substrates biotin and ATP. Here we review the structure and catalytic mechanism of the target enzyme, along with an overview of chemical analogues of biotin and biotinyl-5′-AMP as BPL inhibitors reported to date. Of particular promise are studies to replace the labile phosphoroanhydride linker present in biotinyl-5′-AMP with alternative bioisosteres. A novel in situ click approach using a mutant of S. aureus BPL as a template for the synthesis of triazole-based inhibitors is also presented. These approaches can be widely applied to BPLs from other bacteria, as well as other closely related metabolic enzymes and antibacterial drug targets.
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França A, Pier GB, Vilanova M, Cerca N. Transcriptomic Analysis of Staphylococcus epidermidis Biofilm-Released Cells upon Interaction with Human Blood Circulating Immune Cells and Soluble Factors. Front Microbiol 2016; 7:1143. [PMID: 27493645 PMCID: PMC4955375 DOI: 10.3389/fmicb.2016.01143] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 07/07/2016] [Indexed: 12/27/2022] Open
Affiliation(s)
- Angela França
- Laboratory of Research in Biofilms Rosário Oliveira, Centre of Biological Engineering, University of Minho Braga, Portugal
| | - Gerald B Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School Boston, MA, USA
| | - Manuel Vilanova
- Instituto de Ciências Biomédicas de Abel Salazar, Universidade do PortoPorto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do PortoPorto, Portugal; Instituto de Biologia Molecular e Celular, Universidade do PortoPorto, Portugal
| | - Nuno Cerca
- Laboratory of Research in Biofilms Rosário Oliveira, Centre of Biological Engineering, University of Minho Braga, Portugal
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39
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Kinetic target-guided synthesis in drug discovery and chemical biology: a comprehensive facts and figures survey. Future Med Chem 2016; 8:381-404. [DOI: 10.4155/fmc-2015-0007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
For the last 15 years, kinetic target-guided syntheses, including in situ click chemistry, have been used as alternative methods to find ligands to therapeutically relevant proteins. In this review, a comprehensive survey of biological targets used in kinetic target-guided synthesis covers historical and recent examples. The chemical reactions employed and practical aspects, including controls, library sizes and product detection, are presented. A particular focus is on the reagents and warhead selection and design with a critical overview of the challenges encountered. As protein supply remains a key success factor, it appears that increased efforts should be taken toward miniaturization in order to expand the scope of this strategy and qualify it as a fully fledged drug discovery tool.
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40
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Mechanisms of biotin-regulated gene expression in microbes. Synth Syst Biotechnol 2016; 1:17-24. [PMID: 29062923 PMCID: PMC5640590 DOI: 10.1016/j.synbio.2016.01.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 01/08/2016] [Accepted: 01/10/2016] [Indexed: 12/23/2022] Open
Abstract
Biotin is an essential micronutrient that acts as a co-factor for biotin-dependent metabolic enzymes. In bacteria, the supply of biotin can be achieved by de novo synthesis or import from exogenous sources. Certain bacteria are able to obtain biotin through both mechanisms while others can only fulfill their biotin requirement through de novo synthesis. Inability to fulfill their cellular demand for biotin can have detrimental consequences on cell viability and virulence. Therefore understanding the transcriptional mechanisms that regulate biotin biosynthesis and transport will extend our knowledge about bacterial survival and metabolic adaptation during pathogenesis when the supply of biotin is limited. The most extensively characterized protein that regulates biotin synthesis and uptake is BirA. In certain bacteria, such as Escherichia coli and Staphylococcus aureus, BirA is a bi-functional protein that serves as a transcriptional repressor to regulate biotin biosynthesis genes, as well as acting as a ligase to catalyze the biotinylation of biotin-dependent enzymes. Recent studies have identified two other proteins that also regulate biotin synthesis and transport, namely BioQ and BioR. This review summarizes the different transcriptional repressors and their mechanism of action. Moreover, the ability to regulate the expression of target genes through the activity of a vitamin, such as biotin, may have biotechnological applications in synthetic biology.
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Bockman MR, Kalinda AS, Petrelli R, De la Mora-Rey T, Tiwari D, Liu F, Dawadi S, Nandakumar M, Rhee KY, Schnappinger D, Finzel BC, Aldrich CC. Targeting Mycobacterium tuberculosis Biotin Protein Ligase (MtBPL) with Nucleoside-Based Bisubstrate Adenylation Inhibitors. J Med Chem 2015; 58:7349-7369. [PMID: 26299766 PMCID: PMC4667793 DOI: 10.1021/acs.jmedchem.5b00719] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mycobacterium tuberculosis (Mtb), responsible for both latent and symptomatic tuberculosis (TB), remains the second leading cause of mortality among infectious diseases worldwide. Mycobacterial biotin protein ligase (MtBPL) is an essential enzyme in Mtb and regulates lipid metabolism through the post-translational biotinylation of acyl coenzyme A carboxylases. We report the synthesis and evaluation of a systematic series of potent nucleoside-based inhibitors of MtBPL that contain modifications to the ribofuranosyl ring of the nucleoside. All compounds were characterized by isothermal titration calorimetry (ITC) and shown to bind potently with K(D)s ≤ 2 nM. Additionally, we obtained high-resolution cocrystal structures for a majority of the compounds. Despite fairly uniform biochemical potency, the whole-cell Mtb activity varied greatly with minimum inhibitory concentrations (MIC) ranging from 0.78 to >100 μM. Cellular accumulation studies showed a nearly 10-fold enhancement in accumulation of a C-2'-α analogue over the corresponding C-2'-β analogue, consistent with their differential whole-cell activity.
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Affiliation(s)
- Matthew R. Bockman
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alvin S. Kalinda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA,Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA
| | - Riccardo Petrelli
- Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA
| | - Teresa De la Mora-Rey
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Divya Tiwari
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Feng Liu
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Surrendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Madhumitha Nandakumar
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Kyu Y. Rhee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Barry C. Finzel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA,Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA,Corresponding Author Footnote: To whom correspondence should be addressed. Phone 612-625-7956. Fax 612-626-3114.
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42
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Tieu W, Polyak SW, Paparella AS, Yap MY, Soares da Costa TP, Ng B, Wang G, Lumb R, Bell JM, Turnidge JD, Wilce MCJ, Booker GW, Abell AD. Improved Synthesis of Biotinol-5'-AMP: Implications for Antibacterial Discovery. ACS Med Chem Lett 2015; 6:216-20. [PMID: 25699152 DOI: 10.1021/ml500475n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/11/2014] [Indexed: 11/30/2022] Open
Abstract
An improved synthesis of biotinol-5'-AMP, an acyl-AMP mimic of the natural reaction intermediate of biotin protein ligase (BPL), is reported. This compound was shown to be a pan inhibitor of BPLs from a series of clinically important bacteria, particularly Staphylococcus aureus and Mycobacterium tuberculosis, and kinetic analysis revealed it to be competitive against the substrate biotin. Biotinol-5'-AMP also exhibits antibacterial activity against a panel of clinical isolates of S. aureus and M. tuberculosis with MIC values of 1-8 and 0.5-2.5 μg/mL, respectively, while being devoid of cytotoxicity to human HepG2 cells.
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Affiliation(s)
- William Tieu
- School
of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre
for Molecular Pathology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Steven W. Polyak
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre
for Molecular Pathology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ashleigh S. Paparella
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Min Y. Yap
- School
of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Tatiana P. Soares da Costa
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Belinda Ng
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Geqing Wang
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Richard Lumb
- Microbiology
and Infectious Diseases Directorate, SA Pathology, Women’s and Children’s Hospital, Adelaide, South Australia 5006, Australia
| | - Jan M. Bell
- Microbiology
and Infectious Diseases Directorate, SA Pathology, Women’s and Children’s Hospital, Adelaide, South Australia 5006, Australia
| | - John D. Turnidge
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
- Microbiology
and Infectious Diseases Directorate, SA Pathology, Women’s and Children’s Hospital, Adelaide, South Australia 5006, Australia
| | | | - Grant W. Booker
- School
of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre
for Molecular Pathology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D. Abell
- School
of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre
for Molecular Pathology, The University of Adelaide, Adelaide, South Australia 5005, Australia
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43
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Sittiwong W, Cordonier EL, Zempleni J, Dussault PH. β-Keto and β-hydroxyphosphonate analogs of biotin-5'-AMP are inhibitors of holocarboxylase synthetase. Bioorg Med Chem Lett 2014; 24:5568-5571. [PMID: 25466176 DOI: 10.1016/j.bmcl.2014.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/29/2014] [Accepted: 11/03/2014] [Indexed: 11/15/2022]
Abstract
Holocarboxylase synthetase (HLCS) catalyzes the covalent attachment of biotin to cytoplasmic and mitochondrial carboxylases, nuclear histones, and over a hundred human proteins. Nonhydrolyzable ketophosphonate (β-ketoP) and hydroxyphosphonate (β-hydroxyP) analogs of biotin-5'-AMP inhibit holocarboxylase synthetase (HLCS) with IC50 values of 39.7 μM and 203.7 μM. By comparison, an IC50 value of 7 μM was observed with the previously reported biotinol-5'-AMP. The Ki values, 3.4 μM and 17.3 μM, respectively, are consistent with the IC50 results, and close to the Ki obtained for biotinol-5'-AMP (7 μM). The β-ketoP and β-hydroxyP molecules are competitive inhibitors of HLCS while biotinol-5'-AMP inhibited HLCS by a mixed mechanism.
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Affiliation(s)
- Wantanee Sittiwong
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Elizabeth L Cordonier
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0806, USA
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0806, USA.
| | - Patrick H Dussault
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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44
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Tieu W, Jarrad AM, Paparella AS, Keeling KA, Soares da Costa TP, Wallace JC, Booker GW, Polyak SW, Abell AD. Heterocyclic acyl-phosphate bioisostere-based inhibitors of Staphylococcus aureus biotin protein ligase. Bioorg Med Chem Lett 2014; 24:4689-4693. [DOI: 10.1016/j.bmcl.2014.08.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/07/2014] [Accepted: 08/11/2014] [Indexed: 01/17/2023]
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45
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Shi C, Tiwari D, Wilson DJ, Seiler CL, Schnappinger D, Aldrich CC. Bisubstrate Inhibitors of Biotin Protein Ligase in Mycobacterium tuberculosis Resistant to Cyclonucleoside Formation. ACS Med Chem Lett 2013; 4. [PMID: 24363833 DOI: 10.1021/ml400328a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, is the leading cause bacterial infectious diseases mortality. Biotin protein ligase (BirA) globally regulates lipid metabolism in Mtb through the posttranslational biotinylation of acyl coenzyme A carboxylases (ACCs) involved in lipid biosynthesis and is essential for Mtb survival. We previously developed a rationally designed bisubstrate inhibitor of BirA that displays potent enzyme inhibition and whole-cell activity against multidrug resistant and extensively drug resistant Mtb strains. Here we present the design, synthesis and evaluation of a focused series of inhibitors, which are resistant to cyclonucleoside formation, a key decomposition pathway of our initial analogue. Improved chemical stability is realized through replacement of the adenosyl N-3 nitrogen and C-5' oxygen atom with carbon as well as incorporation of bulky group on the nucleobase to prevent the required syn-conformation necessary for proper alignment of N-3 with C-5'.
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Affiliation(s)
- Ce Shi
- Center
for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Divya Tiwari
- Department
of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Daniel J. Wilson
- Center
for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christopher L. Seiler
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Courtney C. Aldrich
- Center
for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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46
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Pendini NR, Yap MY, Traore DAK, Polyak SW, Cowieson NP, Abell A, Booker GW, Wallace JC, Wilce JA, Wilce MCJ. Structural characterization of Staphylococcus aureus biotin protein ligase and interaction partners: an antibiotic target. Protein Sci 2013; 22:762-73. [PMID: 23559560 DOI: 10.1002/pro.2262] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/26/2013] [Accepted: 03/26/2013] [Indexed: 11/06/2022]
Abstract
The essential metabolic enzyme biotin protein ligase (BPL) is a potential target for the development of new antibiotics required to combat drug-resistant pathogens. Staphylococcus aureus BPL (SaBPL) is a bifunctional protein, possessing both biotin ligase and transcription repressor activities. This positions BPL as a key regulator of several important metabolic pathways. Here, we report the structural analysis of both holo- and apo-forms of SaBPL using X-ray crystallography. We also present small-angle X-ray scattering data of SaBPL in complex with its biotin-carboxyl carrier protein substrate as well as the SaBPL:DNA complex that underlies repression. This has revealed the molecular basis of ligand (biotinyl-5'-AMP) binding and conformational changes associated with catalysis and repressor function. These data provide new information to better understand the bifunctional activities of SaBPL and to inform future strategies for antibiotic discovery.
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Affiliation(s)
- Nicole R Pendini
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria, Australia
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47
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Soares da Costa TP, Yap MY, Perugini MA, Wallace JC, Abell AD, Wilce MCJ, Polyak SW, Booker GW. Dual roles of F123 in protein homodimerization and inhibitor binding to biotin protein ligase fromStaphylococcus aureus. Mol Microbiol 2013; 91:110-20. [DOI: 10.1111/mmi.12446] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2013] [Indexed: 12/17/2022]
Affiliation(s)
| | - Min Y. Yap
- School of Biomedical Science; Monash University; Victoria 3800 Australia
| | - Matthew A. Perugini
- Department of Biochemistry; La Trobe Institute for Molecular Science; La Trobe University; Victoria 3086 Australia
| | - John C. Wallace
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
| | - Andrew D. Abell
- School of Chemistry and Physics; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
| | | | - Steven W. Polyak
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
| | - Grant W. Booker
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
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48
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Tieu W, Soares da Costa TP, Yap MY, Keeling KL, Wilce MCJ, Wallace JC, Booker GW, Polyak SW, Abell AD. Optimising in situ click chemistry: the screening and identification of biotin protein ligase inhibitors. Chem Sci 2013. [DOI: 10.1039/c3sc51127h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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49
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Exploring anti-TB leads from natural products library originated from marine microbes and medicinal plants. Antonie van Leeuwenhoek 2012; 102:447-61. [DOI: 10.1007/s10482-012-9777-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 07/12/2012] [Indexed: 10/28/2022]
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50
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Soares da Costa TP, Tieu W, Yap MY, Zvarec O, Bell JM, Turnidge JD, Wallace JC, Booker GW, Wilce MCJ, Abell AD, Polyak SW. Biotin analogues with antibacterial activity are potent inhibitors of biotin protein ligase. ACS Med Chem Lett 2012; 3:509-14. [PMID: 24900501 DOI: 10.1021/ml300106p] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 05/23/2012] [Indexed: 01/06/2023] Open
Abstract
There is a desperate need to develop new antibiotic agents to combat the rise of drug-resistant bacteria, such as clinically important Staphylococcus aureus. The essential multifunctional enzyme, biotin protein ligase (BPL), is one potential drug target for new antibiotics. We report the synthesis and characterization of a series of biotin analogues with activity against BPLs from S. aureus, Escherichia coli, and Homo sapiens. Two potent inhibitors with K i < 100 nM were identified with antibacterial activity against a panel of clinical isolates of S. aureus (MIC 2-16 μg/mL). Compounds with high ligand efficiency and >20-fold selectivity between the isozymes were identified and characterized. The antibacterial mode of action was shown to be via inhibition of BPL. The bimolecular interactions between the BPL and the inhibitors were defined by surface plasmon resonance studies and X-ray crystallography. These findings pave the way for second-generation inhibitors and antibiotics with greater potency and selectivity.
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Affiliation(s)
| | | | - Min Y. Yap
- School of
Biomedical Science, Monash University,
Victoria, 3800, Australia
| | | | - Jan M. Bell
- Microbiology and Infectious
Diseases Directorate, SA Pathology, Women's and Children's Hospital, South Australia 5006, Australia
| | - John D. Turnidge
- Microbiology and Infectious
Diseases Directorate, SA Pathology, Women's and Children's Hospital, South Australia 5006, Australia
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